Southern Ocean ecosystems are under pressure from resource exploitation and climate change^1,2. Mitigation requires the identification and protection of Areas of Ecological Significance (AESs), which have so far not been determined at the ocean-basin scale. Here, using assemblage-level tracking of marine predators, we identify AESs for this globally important region and assess current threats and protection levels. Integration of more than 4,000 tracks from 17 bird and mammal species reveals AESs around sub-Antarctic islands in the Atlantic and Indian Oceans and over the Antarctic continental shelf. Fishing pressure is disproportionately concentrated inside AESs, and climate change over the next century is predicted to impose pressure on these areas, particularly around the Antarctic continent. At present, 7.1% of the ocean south of 40°S is under formal protection, including 29% of the total AESs. The establishment and regular revision of networks of protection that encompass AESs are needed to provide long-term mitigation of growing pressures on Southern Ocean ecosystems.

Investigations in recent years of the ecological structure and processes of the Southern Ocean have almost exclusively taken a bottom-up, forcing-by-physical-processes approach relating various species' population trends to climate change. Just 20 years ago, however, researchers focused on a broader set of hypotheses, in part formed around a paradigm positing interspecific interactions as central to structuring the ecosystem (forcing by biotic processes, top-down), and particularly on a “krill surplus” caused by the removal from the system of more than a million baleen whales. Since then, this latter idea has disappeared from favour with little debate. Moreover, it recently has been shown that concurrent with whaling there was a massive depletion of finfish in the Southern Ocean, a finding also ignored in deference to climate-related explanations of ecosystem change. We present two examples from the literature, one involving gelatinous organisms and the other involving penguins, in which climate has been used to explain species' population trends but which could better be explained by including species interactions in the modelling. We conclude by questioning the almost complete shift in paradigms that has occurred and discuss whether it is leading Southern Ocean marine ecological science in an instructive direction.

The Retrospective Analysis of Antarctic Tracking Data (RAATD) is a Scientific Committee for Antarctic Research project led jointly by the Expert Groups on Birds and Marine Mammals and Antarctic Biodiversity Informatics, and endorsed by the Commission for the Conservation of Antarctic Marine Living Resources. RAATD consolidated tracking data for multiple species of Antarctic meso- and top-predators to identify Areas of Ecological Significance. These datasets and accompanying syntheses provide a greater understanding of fundamental ecosystem processes in the Southern Ocean, support modelling of predator distributions under future climate scenarios and create inputs that can be incorporated into decision making processes by management authorities. In this data paper, we present the compiled tracking data from research groups that have worked in the Antarctic since the 1990s. The data are publicly available through biodiversity.aq and the Ocean Biogeographic Information System. The archive includes tracking data from over 70 contributors across 12 national Antarctic programs, and includes data from 17 predator species, 4060 individual animals, and over 2.9 million observed locations.